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Agent skill

Bio Consensus Sequences

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus.

No licenceAuto-check passedResearch & Science

Install Bio Consensus Sequences

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-consensus-sequences -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-consensus-sequences --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-consensus-sequences .claude/skills/bio-consensus-sequences && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
bio-consensus-sequences
GitHub stars
3.1k
Used in
1 other repo
Token cost
~2.2k tokens
SKILL.md length
508 words
Files
3
Skills in repo
173
Repo updated
First seen
Licence
None found

At a glance

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus.

  • Creating sample-specific reference sequences
  • SKILL.md covers Version Compatibility, Basic Usage, Haplotype Selection and IUPAC Codes for Heterozygous…, plus 6 more sections
  • Runs Shell scripts from its folder; calls pip
  • Reconstructing haplotypes

What it does

Bio Consensus Sequences is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/generate_consensus.sh` and `usage-guide.md`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Creating sample-specific reference sequences
  • Reconstructing haplotypes

Example prompts

  • “/bio-consensus-sequences”

Requirements

  • Python 3
  • A Bash shell

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Shell), which the agent can run.

    Shell commands in SKILL.md call:

    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Consensus Sequences loads about 2.2k tokens when it runs. Until then it costs about 52 tokens; SKILL.md has 508 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~52
When it runs · the whole SKILL.md, loaded when a task matches
~2.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 508 words (~2,160 tokens).

“Reference examples tested with: BioPython 1.83+, bcftools 1.19+, bedtools 2.31+, minimap2 2.26+, samtools 1.19+”

— opening of SKILL.md by FreedomIntelligence
name
bio-consensus-sequences
tool_type
cli
primary_tool
bcftools

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-consensus-sequences of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/generate_consensus.sh
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Bio Consensus Sequences next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Bio Consensus Sequences compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Consensus Sequences this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~2.2kAutomated safety check: PassNone
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Bio Consensus Sequences

What does Bio Consensus Sequences do?

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Bio Consensus Sequences is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus.

When should I use Bio Consensus Sequences?

Bio Consensus Sequences fits situations like: creating sample-specific reference sequences; reconstructing haplotypes.

How do I install Bio Consensus Sequences in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-consensus-sequences -a claude-code`. Or copy the skill folder (skills/bio-consensus-sequences in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-consensus-sequences in your project. Claude Code loads it when a task matches its description.

How do I install Bio Consensus Sequences in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-consensus-sequences -a codex`. Or copy the skill folder (skills/bio-consensus-sequences in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-consensus-sequences in your project. Codex loads it when a task matches its description.

Can I use Bio Consensus Sequences in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-consensus-sequences -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-consensus-sequences, .gemini/skills/bio-consensus-sequences, .github/skills/bio-consensus-sequences and .opencode/skills/bio-consensus-sequences in your project.

What does Bio Consensus Sequences need to run?

Going by SKILL.md and its folder, Bio Consensus Sequences needs a shell for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3; A Bash shell.

Does Bio Consensus Sequences access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Bio Consensus Sequences safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Consensus Sequences use?

No licence was found for Bio Consensus Sequences or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Consensus Sequences use?

About 2.2k tokens (SKILL.md is roughly 8.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Consensus Sequences?

Skills that share tags, products or a category with Bio Consensus Sequences: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Consensus Sequences?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 skills in this directory. The repository was last updated on July 21, 2026.

Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.